Marley did this a bit too. And he is a teenie puppy! At first, he would sit on the opposite end of the couch and didn't really want to cuddle or sit near me. It's been 5 days since he came here and now he wants to sleep on my head!
She just needs to get used to you, your voice, your smell, the noises in your house. I would say don't force her to cuddle and be loved on if she is really shy and acting upset. Let her tell you when she's ready. You can sit on the floor or the couch and have some yummies and just talk sweetly. Or, if she is REALLY shy just set the treats next to you and ignore her - read a book, watch TV. And let her work up the courage to come get them.
She'll come around! Good luck!